Which organization is responsible for protecting waterways?

The Environmental Protection Agency (EPA) is the organization primarily responsible for protecting waterways in the United States. This agency plays a crucial role in implementing and enforcing federal laws related to water quality and pollution control. The Clean Water Act, one of the key pieces of legislation governing the nation's waters, mandates that the EPA sets water quality standards and regulates discharges into waterways to ensure they are safe and clean.

While other organizations mentioned have relevant functions—like NOAA with marine and atmospheric conditions, OSHA focusing on workplace safety, and the CDC concentrating on public health—none specialize specifically in the protection of waterways to the extent that the EPA does. The primary mission of the EPA revolves around safeguarding water resources, making it the most appropriate choice for this question.